Music apps will add any sound files to their database, including custom ringtones and notification tones that are locally saved. One way to prevent those files from showing up in the database is by using a file manager app to create a blank file titled ".nomedia" (without the quotes, but with the leading period) in that directory. This should hide those files from the Music app, but I'm not sure if that might also hide the files from the system when you're trying to select one of those files as a tone.